Sheep feed and scrapie, France

A Bayesian zero-truncated approach for analysing capture-recapture count data from classical scrapie surveillance in France

Capture-recapture (CR) methods are used to study populations that are monitored with imperfect observation processes. They have recently been applied to the monitoring of animal diseases to evaluate the number of infected units that remain undetected by the surveillance system. This paper proposes three bayesian models to estimate the total number of scrapie-infected holdings in France from CR count data obtained from the French classical scrapie surveillance programme. We fitted two zero-truncated Poisson (ZTP) models (with and without holding size as a covariate) and a zero-truncated negative binomial (ZTNB) model to the 2006 national surveillance count dataset. We detected a large amount of heterogeneity in the count data, making the use of the simple ZTP model inappropriate. However, including holding size as a covariate did not bring any significant improvement over the simple ZTP model. The ZTNB model proved to be the best model, giving an estimation of 535 (CI(95%) 401-796) infected and detectable sheep holdings in 2006, although only 141 were effectively detected, resulting in a holding-level prevalence of 4.4‰ (CI(95%) 3.2-6.3) and a sensitivity of holding-level surveillance of 26% (CI(95%) 18-35). The main limitation of the present study was the small amount of data collected during the surveillance programme. It was therefore not possible to build complex models that would allow depicting more accurately the epidemiological and detection processes that generate the surveillance data. We discuss the perspectives of capture-recapture count models in the context of animal disease surveillance.

A case-control study of atypical scrapie in GB sheep flocks

Wide-scale scrapie surveillance started in 2002 in the EU. As a result, a new form of scrapie was detected which has been referred to as atypical scrapie. Here we present a case-control study conducted on British sheep farms to increase our understanding of the disease and potential risk factors at holding level. Forty case and 120 control holdings were traced from the confirmed atypical results in the scrapie surveillance programme in Great Britain during the period 2002-2007. A detailed questionnaire was completed by interview to record data on holding-specific management variables. A combination of generalized additive, generalized linear and Bayesian models returned 3 variables clearly associated with an increase in the odds of atypical scrapie: presence of two sheep breeds (Welsh Mountain and Cheviot) and flock type (store/fattening flocks). A fourth variable, the number of visits by veterinarians to the holding exerted a protective effect. Various other variables were significantly associated with the outcome, but at a somewhat lower level of confidence; for example, the size of the holding and the presence on the farm of concentrates intended for animals other than sheep.

Scrapie prevalence in sheep of susceptible genotype is declining in a population subject to breeding for resistance

Background

Susceptibility of sheep to scrapie infection is known to be modulated by the PrP genotype of the animal. In the Netherlands an ambitious scrapie control programme was started in 1998, based on genetic selection of animals for breeding. From 2002 onwards EU regulations required intensive active scrapie surveillance as well as certain control measures in affected flocks.

Here we analyze the data on genotype frequencies and scrapie prevalence in the Dutch sheep population obtained from both surveillance and affected flocks, to identify temporal trends. We also estimate the genotype-specific relative risks to become a detected scrapie case.

Results

We find that the breeding programme has produced a steady increase in the level of genetic scrapie resistance in the Dutch sheep population. We also find that a significant decline in the prevalence of scrapie in tested animals has occurred a number of years after the start of the breeding programme. Most importantly, the estimated scrapie prevalence level per head of susceptible genotype is also declining significantly, indicating that selective breeding causes a population effect.

Conclusions

The Dutch scrapie control programme has produced a steady rise in genetic resistance levels in recent years. A recent decline in the scrapie prevalence per tested sheep of susceptible prion protein genotype indicates that selective breeding causes the desired population effect.

The evaluation of exposure risks for natural transmission of scrapie within an infected flock

Background

Although the epidemiology of scrapie has been broadly understood for many years, attempts to introduce voluntary or compulsory controls to eradicate the disease have frequently failed. Lack of precision in defining the risk factors on farm has been one of the challenges to designing control strategies. This study attempted to define which parts of the annual flock management cycle represented the greatest risk of infection to naive lambs exposed to the farm environment at different times.

Results

In VRQ/VRQ lambs exposed to infected sheep at pasture or during lambing, and exposed to the buildings in which lambing took place, the attack rate was high and survival times were short. Where exposure was to pasture alone the number of sheep affected in each experimental group was reduced, and survival times were longer and related to length of exposure.

Conclusion

At the flock level, eradication and control strategies for scrapie must take into account the need to decontaminate buildings used for lambing, and to reduce (or prevent) the exposure of lambs to infected sheep, especially in the later stages of incubation, and at lambing. The potential for environmental contamination from pasture should also be considered. Genotype selection may still prove to be the only viable tool to prevent infection from contaminated pasture, reduce environmental contamination and limit direct transmission from sheep to sheep.

Classical sheep scrapie in Great Britain: spatial analysis and identification of environmental and farm-related risk factors

BACKGROUND

Previous studies suggest that the spatial distribution of classical sheep scrapie in Great Britain is uneven and that certain flock characteristics may be associated with occurrence of the disease. However, the existence of areas of high and low disease-risk may also result from differences in the spatial distribution of environmental characteristics. In this study we explored the spatial pattern of classical scrapie in Great Britain between 2002 and 2005 and investigated the association between disease occurrence and various environmental and farm-related risk factors.

RESULTS

Exploratory spatial analysis: South Wales was found to have a higher density of scrapie-positive farms than the rest of Great Britain. In addition, a small cluster of high-risk farms was identified in the center of this region in which clustering of scrapie-positive farms occurred up to a distance of approximately 40 km. SPATIAL MODELLING: A mixed-effects regression model identified flock-size and soil drainage to be significantly associated with the occurrence of scrapie in England and Wales (area under the curve (AUC) 0.71 +/- 0.01, 95% CI 0.68 - 0.74). The predictive risk map based on the estimated association between these factors and disease occurrence showed most of Wales to be at risk of being confirmed positive for scrapie with areas of highest risk in central and south Wales. In England, areas with the highest risk occurred mainly in the north and the midlands.

CONCLUSION

The observed distribution of scrapie in Great Britain exhibited a definite spatial pattern with south Wales identified as an area of high occurrence. In addition both flock (flock size) and environmental variables (soil drainage) were found to be significantly associated with the occurrence of the disease. However, the model's AUC indicated unexplained variation remaining in the model and the source of this variation may lie in farm-level characteristics rather than spatially-varying ones such as environmental factors.

A case-control study on the origin of atypical scrapie in sheep, France

Risk factors for this disease suggest a noninfectious origin influenced by genetic and metabolic factors.

A matched case–control study (95 cases and 220 controls) was designed to study risk factors for atypical scrapie in sheep in France. We analyzed contacts with animals from other flocks, lambing and feeding practices, and exposure to toxic substances. Data on the prnp genotype were collected for some case and control animals and included in a complementary analysis. Sheep dairy farms had a higher risk for scrapie (odds ratio [OR] 15.1, 95% confidence interval [CI] 3.3–69.7). Lower risk was associated with organic farms (OR 0.15, 95% CI 0.02–1.26), feeding corn silage (OR 0.16, 95% CI 0.05–0.53), and feeding vitamin and mineral supplements (OR 0.6, 95% CI 0.32–1.14). Genetic effects were quantitatively important but only marginally changed estimates of other variables. We did not find any risk factor associated with an infectious origin of scrapie. Atypical scrapie could be a spontaneous disease influenced by genetic and metabolic factors.

A descriptive study of the prevalence of atypical and classical scrapie in sheep in 20 European countries

Background

The development of active surveillance programmes for transmissible spongiform encephalopathies of small ruminants across Europe has led to the recent identification of a previously undetected form of ovine prion disease, 'atypical' scrapie. Knowledge of the epidemiology of this disease is still limited, as is whether it represents a risk for animal and/or public health.

The detection of atypical scrapie has been related to the use of only some of the EU agreed rapid tests. Information about the rapid tests used is not, as yet, available from public reports on the surveillance of transmissible spongiform encephalopathies in small ruminants. We collected detailed results of active surveillance from European countries to estimate and to compare the prevalence of atypical scrapie and classical scrapie in sheep for each country stratified by each surveillance stream; healthy slaughtered and found dead adult sheep.

Results

From the 20 participating countries, it appeared that atypical scrapie was detected in Europe wherever the conditions necessary for its diagnosis were present. In most countries, atypical scrapie and classical scrapie occurred at low prevalence level. The classical scrapie prevalence estimates were more variable than those for atypical scrapie, which appeared remarkably homogeneous across countries, surveillance streams and calendar years of surveillance. Differences were observed in the age and genotype of atypical scrapie and classical scrapie cases that are consistent with previous published findings.

Conclusion

This work suggests that atypical scrapie is not rare compared to classical scrapie. The homogeneity of its prevalence, whatever the country, stream of surveillance or year of detection, contrasts with the epidemiological pattern of classical scrapie. This suggests that the aetiology of atypical scrapie differs from that of classical scrapie.

Atypical bovine spongiform encephalopathies, France, 2001-2007

In France, through exhaustive active surveillance, ≈17.1 million adult cattle were tested for bovine spongiform encephalopathy from July 2001 through July 2007; ≈3.6 million were >8 years of age. Our retrospective Western blot study of all 645 confirmed cases found that 7 were H-type and 6 were L-type.

Bovine Spongiform Encephalopathy and Spatial Analysis of the Feed Industry

In France, despite the ban of meat-and-bone meal (MBM) in cattle feed, bovine spongiform encephalopathy (BSE) was detected in hundreds of cattle born after the ban. To study the role of MBM, animal fat, and dicalcium phosphate on the risk for BSE after the feed ban, we conducted a spatial analysis of the feed industry. We used data from 629 BSE cases as well as data on use of each byproduct and market area of the feed factories. We mapped risk for BSE in 951 areas supplied by the same factories and connection with use of byproducts. A disease map of BSE with covariates was built with the hierarchical Bayesian modeling methods, based on Poisson distribution with spatial smoothing. Only use of MBM was spatially linked to risk for BSE, which highlights cross-contamination as the most probable source of infection after the feed ban.

Milk yield, age at first calving, and the risk of BSE: An analysis at the farm level in France

The epidemic of bovine spongiform encephalopathy (BSE) in France, as in the UK, has affected dairy cattle much more than beef cattle. However, the intensification of dairy herd management as a risk factor for BSE has not to date been analyzed. For this purpose, two databases were merged: the French Milk Records database, and the French BSE database, which can be considered as being devoid of notification bias since July 2001, when systematic tests were implemented. Only pure Holstein herds were considered, which represent the vast majority of total and BSE-affected dairy herds in France. A case-control study was designed so that 20 control herds were matched to each case herd according to the location of the farm and the year of birth of the index case. Three thousand and forty five farms were included, among which 145 with a BSE case notified between July 2001 and July 2003, and 2900 controls. With respect to the risk of BSE, odds ratios for each class of milk yield and age at first calving were estimated by using conditional logistic regression models with appropriate adjustments to herd size. The two main results were the following: firstly, whereas most Holstein herds, with average production between 7000 and 10,000kg, had nearly the same BSE risk, a small category of very intensive herds, with annual milk yields above 10,000kg, were significantly more at risk than the other herds. Secondly, a very early first calving (under 26 months of age) was found to be at risk for BSE as compared to other categories, independently of the milk yield. These results are discussed in the light of the known age-dependent susceptibility to BSE.

A case–control study of scrapie Nor98 in Norwegian sheep flocks

Scrapie is a fatal, neurological disease of sheep and goats and belongs to the transmissible spongiform encephalopathies. In 1998, a new type of scrapie, designated scrapie Nor98, was detected in Norway. Scrapie Nor98 differs from classical scrapie in the distribution of pathological changes and of the scrapie prion protein, the Western blot profile of the prion protein, and with isolated cases usually being observed in the case flocks. In 2004, a case–control study was conducted on scrapie Nor98 with 28 cases and 102 randomly selected controls. The questionnaire included questions on demographic data, animal contact between sheep flocks, indirect contact with equipment, use of concentrate feed and supplemental feeds, and use of medicines and vaccines. The data were analysed by using logistic regression with the sheep flock as the statistical unit. In the final model, the detection of scrapie Nor98 was related to the practice of not removing all afterbirths, the use of vitamin and mineral feed supplements, the absence of concentrate feed of swine or poultry on the farm and the presence of dogs on the farm. The results show that the epidemiology of scrapie Nor98 differs from that of classical scrapie in that no risk factors that indicate transmission of scrapie Nor98 between flocks by movement or direct contact between animals were found. Furthermore, the association between scrapie Nor98 and mineral intake shown herein should be explored further. Although the possibility that scrapie Nor98 has a low transmissibility between animals under natural conditions cannot be ruled out, the results would also be in accordance with a spontaneous aetiology.

Flock-level risk factors for scrapie in Great Britain: analysis of a 2002 anonymous postal survey

Background

In November 2002, an anonymous postal survey of sheep farmers in Great Britain (GB) was conducted to identify factors associated with the flock-level occurrence of scrapie. This survey was undertaken to update an earlier postal survey in 1998, and was the first occasion in which a large-scale postal survey had been repeated.

Results

The results of the 2002 survey indicated that scrapie was more likely to occur in certain geographic regions; in purebred compared to commercial flocks; in larger flocks; in flocks which lambed in group pens compared to those which lambed in individual pens; in flocks which always lambed in the same location compared to those which did not; and in farms which kept certain breeds of sheep. In addition to these factors, the likelihood of the disease occurring in homebred animals was higher in flocks which bred a greater proportion of replacement animals or which bought-in lambs. Finally, within-flock transmission following exposure was more likely to occur in hill flocks compared to other farm types; in flocks which bred a greater proportion of replacement animals; and in farms which kept a certain crossbreed of ewe.

Conclusion

The risk factors identified from the 1998 and 2002 anonymous postal surveys in Great Britain were similar. However, differences between the surveys were identified in the influence of region and of purchasing behaviour on the risk of scrapie. These differences are most likely a consequence of changes in farmer awareness and the impact of the 2001 foot-and-mouth disease epidemic, respectively.